RetrogeneDB ID: retro_tbel_1370

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4515:181095..181467(+)
• Located in intron of: ENSTBEG00000012411

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PAIP2
• Ensembl ID: ENSTBEG00000004105
• Aliases: None
• Description: poly(A) binding protein interacting protein 2 [Source:HGNC Symbol;Acc:17970]

Sequence

>retro_tbel_1370
ATGAAAGATCTAAGTCGCAGCAGTACTAGCCCAAGCATCGTCAATGAGGATGTGATTATTAACGATCGTTCTCATGAAGA
CGACAATCCATTTGCAGACTACATGCGGAAGGAACATGAAGAGAAATTCAATAGACAAACAGAGGAGGAGTTATGGGAAG
AGGAATTTATTGAATGCTGTTTCCAAGAAATGCTGGAAGAGGAAGTAGAACATGAGTGGTACATTCCAGCTCGAGATCTC
CCACAAACTGTGGACCAAATCCAAGAGCAGTTTAATGACCTTGTTATCAGTGATGGCTCTTCTCAGGAAGATCTTGCAGT
CAAGAGGAATCTAAATCCAGATGCAAAGGAGTTTGCTCCTGGGGTGAAGTAC

Alignment

ORF - retro_tbel_1370 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.87 %
• Parental protein coverage: 98.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKDPSRSSTSPSIINEDVIINGHSHEDDNPFAEYMWMENEEEFNRQIEEELWEEEFIERCFQEMLEEEEE
          MKD.SRSSTSPSI.NEDVIIN..SHEDDNPFA.YM..E.EE.FNRQ.EEELWEEEFIE.CFQEMLEEE.E
Retrocopy MKDLSRSSTSPSIVNEDVIINDRSHEDDNPFADYMRKEHEEKFNRQTEEELWEEEFIECCFQEMLEEEVE

Parental  HEWFIPARDLPQTMDQIQDQFNDLVISDGSSLEDLVVKSNLNPNAKEFVPGVKY
          HEW.IPARDLPQT.DQIQ.QFNDLVISDGSS.EDL.VK.NLNP.AKEF.PGVKY
Retrocopy HEWYIPARDLPQTVDQIQEQFNDLVISDGSSQEDLAVKRNLNPDAKEFAPGVKY

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_1370 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1370 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006982	1 retrocopy	retro_cjac_212,
Dipodomys ordii	ENSDORG00000002264	1 retrocopy	retro_dord_676,
Microcebus murinus	ENSMICG00000012451	1 retrocopy	retro_mmur_1085,
Rattus norvegicus	ENSRNOG00000019934	1 retrocopy	retro_rnor_294,
Tupaia belangeri	ENSTBEG00000004105	1 retrocopy	retro_tbel_1370 ,